DOCSLIB.ORG

NCBI Database on Cycloartenol Synthase

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

NCBI Database on Cycloartenol Synthase Mohammad Basyuni1,2, Rahmah Hayati1, Yuntha Bimantara1, Rizka Amelia1, Sumaiyah3, Era Yusraini4, and Hirosuke Oku5 1Department of Forestry, Faculty of Forestry, Universitas Sumatera Utara, Jl. Tri Dharma Ujung No. 1 Medan, North Sumatera 20155, Indonesia 2Mangrove and Bio-Resources Group, Center of Excellence for Natural Resources Based Technology, Universitas Sumatera Utara, Medan North Sumatera 20155, Indonesia. 3Faculty of Pharmacy, Universitas Sumatera Utara, Medan 20155, Indonesia 4Faculty of Agriculture, Universitas Sumatera Utara, Medan 20155, Indonesia 3Molecular Biotechnology Group, Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan Keywords: Abiotic stress, cycloartenol, isoprenoid, oxidosqualene Abstract: Cycloartenol synthase (EC 5.4.99.8) is a cycloartenol-converting enzyme. The current research describes the search of cycloartenol synthase databases from the National Center for Biotechnology Information (NCBI). A amount of precious information was generated by NCBI database search (https:/www.ncbi.nlm.nih.gov/). Results discovered in 22 cycloartenol synthase databases. All literature, genes, genetics, protein, genomes, and chemical features of cycloartenol synthase databases. Bookshelf, MeSH (Medical Subject Headings) and PubMed Central were discussed in the literature. Gene was made up of profiles from Gene, Gene Expression Omnibus (GEO), HomoloGene, PopSet, and UniGene. Data on genetics such as MedGen was available for cycloartenol synthase. Proteins characteristic comprised Conserved Domains, Identical groups of proteins, clusters of proteins, sparcle, and structure. Nucleotide and sample were engaged in genomes. BioSystems, PubChem BioAssay, PubChem Compound, and PubChem Substance are the chemical properties. The present work affords vital information in term biotechnology of cycloartenol synthase. 1 INTRODUCTION are accountable for biosynthesis of phytosterol, and more OSCs are committed for triterpene Phytosterol including cycloartenol is ordinary synthesis (Thimmappa et al., 2014). chemical constituents in higher plants (Augustin et Lanosterol and cycloartenol are significant al., 2011; Uddin et al., 2015). Phytosterols serve as elements of the membrane and can provide chemotaxonomy markers also have been shown substrates for hormones of sterols (Bloch 1983). (Koch et al., 2011). Many phylogenetic analyses Our previous studies have shown that membrane have been suggested that plant oxidosqualene lipids (triterpenoids and phytosterols) have an cyclases (OSCs) are generally evolutionarily evident role in mangrove modification to salinity derived from cycloartenol synthase (Zhang et al., stress (Oku et al., 2003; Basyuni et al., 2009, 2003; Basyuni et al., 2007a,b). More than 2012a,b), Saccharomyces cerevisiae, GIL77, thousands different OSC genes together with modulated the salt tolerance of lanosterol synthase cycloartenol have been reported from plant deficient (Inafuku et al., 2018). Even though a kingdom, which are expanded from a shared 2,3- significant number of studies in cycloartenol oxidosqualene substrate via OSCs, they separate in synthases have been well documented (Agustin et the cyclization of this intermediacy into each of al., 2011; Xue et al., 2012; Gas-Pascual et al., phytosterol of cycloartenol and lanosterol or a 2014; Moses et al., 2014; Thimmappa et al., 2014;), diversity of triterpenes (Augustin et al., 2011). In Limited work concentrated on biotechnology data plantae, cycloartenol synthase (CAS) along with from all accessible databases in cycloartenol lanosterol synthase (LAS), family member of OSC synthases. Here we report an alternative technique 16 Basyuni, M., Hayati, R., Bimantara, Y., Amelia, R., Sumaiyah, S., Yusraini, E. and Oku, H. NCBI Database on Cycloartenol Synthase. DOI: 10.5220/0008386800160019 In Proceedings of the International Conference on Natural Resources and Technology (ICONART 2019), pages 16-19 ISBN: 978-989-758-404-6 Copyright c 2019 by SCITEPRESS – Science and Technology Publications, Lda. All rights reserved NCBI Database on Cycloartenol Synthase to collect useful data needed in latest Furthermore, 87 Pubmed and 232 PubMed Central biotechnology-related science studies on documentations were stored as called the plant cycloartenol synthase through a preferred search cycloartenol synthase (Table 1). The PubMed engine. Therefore, the aim of this research was to database includes quotes derived different topics in explain the implementation of the National Center many connections to reports of full-text papers on for Biotechnology Information (NCBI) databases rubber plants open access. (GQuery) search to gain more deepful information on updated cycloartenol synthesis biotechnology. Table 2: Genes source NCBI database for cycloartenol synthase Health Amount Explanation 2 MATERIALS AND METHODE Gene 242 Gathered data about the gene loci GEO Profiles 116 Gene profile and molecular The search engine for NCBI databases abundance patterns (https:/www.ncbi.nlm.nih.gov/) was used to HomoloGene 2 Homologous gene sets for produce a amount of useful rubber plant data chosen organisms biotechnology. As stated previously on September PopSet 3 Sets of phylogenetic and population studies sequences 19, 2018, data bases were obtained by writing UniGene 66 Groups of transcripts Hevea brasiliensis in all database searches. All conveyed databases composed of literature, health, genes, protein, genomes, and chemical properties were Table 3: Genetics source NCBI database for cycloartenol featured. Cycloartenol synthase (GQuery) was synthase performed. The bookshelf, MeSH (Medical Genetics Total Information Subject Headings), NLM (National Medicine MedGen 1 Literature and connections in Library) Catalog, PubMed, PubMed Central, EST, medical genetics Gene, GEO datasets, PopSet, Identical Protein Groups, Protein, Sparde, Structure, Assembly, Table 4: Proteins source NCBI database for cycloartenol BioProject, BioSample, Genome, GSS, Nucleotide, synthase Probe, SRA, Taxonomy, Biosystems, and Proteins Number Explanation PubChem BioAssay were the data variables. Conserved 1 Preserved protein domains Domains Identical 723 Sequences of proteins Protein classified by similarity 3 RESULTS AND DISCUSSIONS Groups Protein 976 Sequences of proteins Table 1 demonstrates the literature on cycloartenol Protein 17 Sequence of protein clusters synthase available in the NCBI. Four biographies Clusters based on similarity Structure 2 Experimentally determined stored in countless numbers. The web NCBI biomolecular structures literature provides internet libraries and free access to bookshelf data (two reports and books), 2 MeSH Table 5: Genomes source NCBI database for Plant and (Medical Subject Headings), namely cycloartenol cycloartenol synthase synthase [Supplementary Concept] and 3-beta-(2- (diethylamino) ethoxy) androst-5-en-17-one [ Genomes Number Description Nucleotide 1583 RNA and DNA sequences Additional Concept], ontology used to index PubMed papers. Probe 92 Biomolecular structures experimentally determined Table 1: Literature source NCBI database for cycloartenol synthase Information on genes sources is displayed in Literature Total Information Table 2. This data is as well as genes associated to Bookshelf 2 Reports and books cycloartenol synthase than consisting of 242 genes Mesh 2 Medical topic in the with top organisms are Rosa chinensis (15), Malus collections of the NLM domestica (14), Camellia sinensis (11), Zea mays PubMed 312 Scientific and medical (10), Pyrus x bretschneideri (10), Gossypium abstracts/quotations PubMed 584 Articles in full-text journals hirsutum (10), G. raimondii (10), Vitis vinifera Central (10), Aegilops tauschii (8), Arachis hypogaea (8), 17 ICONART 2019 - International Conference on Natural Resources and Technology Brachypodium distachyon (7), Phoenix dactylifera Biosystems, 107 PubChem bioassay, 22 PubChem (7), Nicotiana tabacum (7), and all other taxa. compound, and 58 PubChem substance. Table 2 shows there is 116 GEO profiles, one homologene, three popset, and 66 uniges. It is Table 6: Chemicals source NCBI database for important to note that top organisms for unigene cycloartenol synthase are Malus domestica (5), Zea mays (5), Panicum Chemicals Total Information virgatum (4), Brassica napus (3), Arabidopsis BioSystems 10234 Molecular pathways thaliana (3), Citrus sinensis (3), Medicago associated to genes, proteins truncatula (3), Vitis vinifera (3), Triticum aestivum and chemicals (3), and Pinus taeda (3). The three popsets are PubChem 107 Bioactivity screening Nicotiana tabacum cycloartenol synthase (CAS1) BioAssay PubChem 22 Chemical data with systems, mRNA, complete cds, Bacillariophyta cycloartenol Compound experience and relationships synthase gene, partial cds, and Avena cycloartenol synthase gene, complete cds. PubChem 58 Substance stored and Table 3 shows one genetics information on Substance chemical data medical genetics literature and links. On the other hand, Table 4 depicts protein source from NCBI Protein modeling of cycloartenol synthase from database for there are five sources for protein that mangrove trees has recently been defined (Basyuni consists of one conserved domain, 723 identical et al. 2018). The protein modeling for KcCAS in protein groups, 976 proteins, 17 protein clusters, Kandelia candel and RsCAS of Rhizophora stylosa and two structures. The conserved domains cycloartenol synthases was analyzed by Pyre2 comprise C-terminal
Recommended publications
  • Analysis of the Chromosomal Clustering of Fusarium-Responsive

    Analysis of the Chromosomal Clustering of Fusarium-Responsive

    www.nature.com/scientificreports OPEN Analysis of the chromosomal clustering of Fusarium‑responsive wheat genes uncovers new players in the defence against head blight disease Alexandre Perochon1,2, Harriet R. Benbow1,2, Katarzyna Ślęczka‑Brady1, Keshav B. Malla1 & Fiona M. Doohan1* There is increasing evidence that some functionally related, co‑expressed genes cluster within eukaryotic genomes. We present a novel pipeline that delineates such eukaryotic gene clusters. Using this tool for bread wheat, we uncovered 44 clusters of genes that are responsive to the fungal pathogen Fusarium graminearum. As expected, these Fusarium‑responsive gene clusters (FRGCs) included metabolic gene clusters, many of which are associated with disease resistance, but hitherto not described for wheat. However, the majority of the FRGCs are non‑metabolic, many of which contain clusters of paralogues, including those implicated in plant disease responses, such as glutathione transferases, MAP kinases, and germin‑like proteins. 20 of the FRGCs encode nonhomologous, non‑metabolic genes (including defence‑related genes). One of these clusters includes the characterised Fusarium resistance orphan gene, TaFROG. Eight of the FRGCs map within 6 FHB resistance loci. One small QTL on chromosome 7D (4.7 Mb) encodes eight Fusarium‑ responsive genes, fve of which are within a FRGC. This study provides a new tool to identify genomic regions enriched in genes responsive to specifc traits of interest and applied herein it highlighted gene families, genetic loci and biological pathways of importance in the response of wheat to disease. Prokaryote genomes encode co-transcribed genes with related functions that cluster together within operons. Clusters of functionally related genes also exist in eukaryote genomes, including fungi, nematodes, mammals and plants1.
  • Next-Generation Sequencing of Representational Difference Analysis

    Next-Generation Sequencing of Representational Difference Analysis

    Planta DOI 10.1007/s00425-017-2657-0 ORIGINAL ARTICLE Next-generation sequencing of representational difference analysis products for identification of genes involved in diosgenin biosynthesis in fenugreek (Trigonella foenum-graecum) 1 1 1 1 Joanna Ciura • Magdalena Szeliga • Michalina Grzesik • Mirosław Tyrka Received: 19 August 2016 / Accepted: 30 January 2017 Ó The Author(s) 2017. This article is published with open access at Springerlink.com Abstract Within the transcripts related to sterol and steroidal Main conclusion Representational difference analysis saponin biosynthesis, we discovered novel candidate of cDNA was performed and differential products were genes of diosgenin biosynthesis and validated their sequenced and annotated. Candidate genes involved in expression using quantitative RT-PCR analysis. Based on biosynthesis of diosgenin in fenugreek were identified. these findings, we supported the idea that diosgenin is Detailed mechanism of diosgenin synthesis was biosynthesized from cycloartenol via cholesterol. This is proposed. the first report on the next-generation sequencing of cDNA-RDA products. Analysis of the transcriptomes Fenugreek (Trigonella foenum-graecum L.) is a valuable enriched in low copy sequences contributed substantially medicinal and crop plant. It belongs to Fabaceae family to our understanding of the biochemical pathways of and has a unique potential to synthesize valuable steroidal steroid synthesis in fenugreek. saponins, e.g., diosgenin. Elicitation (methyl jasmonate) and precursor feeding (cholesterol and squalene) were Keywords Diosgenin Á Next-generation sequencing Á used to enhance the content of sterols and steroidal Phytosterols Á Representational difference analysis of sapogenins in in vitro grown plants for representational cDNA Á Steroidal saponins Á Transcriptome user-friendly difference analysis of cDNA (cDNA-RDA).
  • Allelic Mutant Series Reveal Distinct Functions for Arabidopsis Cycloartenol Synthase 1 in Cell Viability and Plastid Biogenesis

    Allelic Mutant Series Reveal Distinct Functions for Arabidopsis Cycloartenol Synthase 1 in Cell Viability and Plastid Biogenesis

    Allelic mutant series reveal distinct functions for Arabidopsis cycloartenol synthase 1 in cell viability and plastid biogenesis Elena Babiychuk*†, Pierrette Bouvier-Nave´ ‡, Vincent Compagnon‡, Masashi Suzuki§, Toshiya Muranaka§, Marc Van Montagu*†¶, Sergei Kushnir*†, and Hubert Schaller‡¶ *Department of Plant Systems Biology, Flanders Institute for Biotechnology, Technologiepark 927, 9052 Ghent, Belgium; †Department of Molecular Genetics, Ghent University, 9052 Ghent, Belgium; ‡Institut de Biologie Mole´culaire des Plantes, Centre National de la Recherche Scientifique–Unite´ Propre de Recherche 2357, Universite´Louis Pasteur, 28 rue Goethe, 67083 Strasbourg, France; and §RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan Contributed by Marc Van Montagu, December 24, 2007 (sent for review August 31, 2007) Sterols have multiple functions in all eukaryotes. In plants, sterol biosynthesis is initiated by the enzymatic conversion of 2,3-oxido- squalene to cycloartenol. This reaction is catalyzed by cycloartenol synthase 1 (CAS1), which belongs to a family of 13 2,3-oxidosqua- lene cyclases in Arabidopsis thaliana. To understand the full scope of sterol biological functions in plants, we characterized allelic series of cas1 mutations. Plants carrying the weak mutant allele cas1–1 were viable but developed albino inflorescence shoots because of photooxidation of plastids in stems that contained low amounts of carotenoids and chlorophylls. Consistent with the CAS1 catalyzed reaction, mutant tissues accumulated 2,3-oxidosqualene. This triterpenoid precursor did not increase at the expense of the pathway end products. Two strong mutations, cas1–2 and cas1–3, were not transmissible through the male gametes, suggesting a role for CAS1 in male gametophyte function. To validate these findings, we analyzed a conditional CRE/loxP recombination- dependent cas1–2 mutant allele.
  • The Role of LC and FAS in Regulating Floral Meristem and Fruit Locule Number in Tomato

    The Role of LC and FAS in Regulating Floral Meristem and Fruit Locule Number in Tomato

    The role of LC and FAS in regulating floral meristem and fruit locule number in tomato Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Yi-Hsuan Chu, B.S. Graduate Program in Horticulture and Crop Science The Ohio State University 2017 Dissertation Committee Dr. Jyan-Chyun Jang, Dr. Esther van der Knaap, Advisor Dr. Anna Dobritsa Dr. David Mackey Dr. Leah McHale 1 Copyrighted by Yi-Hsuan Chu 2017 2 Abstract In tomato, lc and fas control the variation between the small and bilocular fruits from the wild ancestor (S. pimpinellifolium) and large fruit cultivars (S. lycopersicum var. lycopersicum) with up to ten locules. SlWUS and SlCLV3 are the candidates of lc and fas, respectively. The regulatory balance between these two genes plays a pivotal role in meristem maintenance in Arabidopsis. However, the genetic and molecular mechanisms of SlWUS and SlCLV3 have not been functionally characterized in tomato. Here, we performed a detailed phenotypic analysis of the reproductive organs in tomato near-isogenic lines. The results showed that lc and fas synergistically controlled floral organ and locule number. In addition, results from targeted RNA interference (RNAi) and transgenic complementation of fas clearly demonstrated that SlCLV3 was the gene underlying fas. By using mRNA in situ hybridization and transcriptome profiling, we observed temporal and spatial changes in the expression patterns of these two genes during floral development. Our results indicated that lc was a gain-of-function mutation of SlWUS while fas was a loss-of-function mutation of SlCLV3.
  • Friedelin Synthase from Maytenus Ilicifolia

    Friedelin Synthase from Maytenus Ilicifolia

    www.nature.com/scientificreports OPEN Friedelin Synthase from Maytenus ilicifolia: Leucine 482 Plays an Essential Role in the Production of Received: 09 May 2016 Accepted: 20 October 2016 the Most Rearranged Pentacyclic Published: 22 November 2016 Triterpene Tatiana M. Souza-Moreira1, Thaís B. Alves1, Karina A. Pinheiro1, Lidiane G. Felippe1, Gustavo M. A. De Lima2, Tatiana F. Watanabe1, Cristina C. Barbosa3, Vânia A. F. F. M. Santos1, Norberto P. Lopes4, Sandro R. Valentini3, Rafael V. C. Guido2, Maysa Furlan1 & Cleslei F. Zanelli3 Among the biologically active triterpenes, friedelin has the most-rearranged structure produced by the oxidosqualene cyclases and is the only one containing a cetonic group. In this study, we cloned and functionally characterized friedelin synthase and one cycloartenol synthase from Maytenus ilicifolia (Celastraceae). The complete coding sequences of these 2 genes were cloned from leaf mRNA, and their functions were characterized by heterologous expression in yeast. The cycloartenol synthase sequence is very similar to other known OSCs of this type (approximately 80% identity), although the M. ilicifolia friedelin synthase amino acid sequence is more related to β-amyrin synthases (65–74% identity), which is similar to the friedelin synthase cloned from Kalanchoe daigremontiana. Multiple sequence alignments demonstrated the presence of a leucine residue two positions upstream of the friedelin synthase Asp-Cys-Thr-Ala-Glu (DCTAE) active site motif, while the vast majority of OSCs identified so far have a valine or isoleucine residue at the same position. The substitution of the leucine residue with valine, threonine or isoleucine in M. ilicifolia friedelin synthase interfered with substrate recognition and lead to the production of different pentacyclic triterpenes.
  • Comparative Characterization of the Leaf Tissue of Physalis Alkekengi and Physalis Peruviana Using RNA-Seq and Metabolite Profiling

    Comparative Characterization of the Leaf Tissue of Physalis Alkekengi and Physalis Peruviana Using RNA-Seq and Metabolite Profiling

    fpls-07-01883 December 17, 2016 Time: 17:38 # 1 ORIGINAL RESEARCH published: 20 December 2016 doi: 10.3389/fpls.2016.01883 Comparative Characterization of the Leaf Tissue of Physalis alkekengi and Physalis peruviana Using RNA-seq and Metabolite Profiling Atsushi Fukushima1*, Michimi Nakamura2, Hideyuki Suzuki3, Mami Yamazaki2, Eva Knoch1, Tetsuya Mori1, Naoyuki Umemoto1, Masaki Morita4, Go Hirai4,5, Mikiko Sodeoka4,5 and Kazuki Saito1,2* 1 RIKEN Center for Sustainable Resource Science, Yokohama, Japan, 2 Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan, 3 Department of Biotechnology Research, Kazusa DNA Research Institute, Chiba, Japan, 4 Synthetic Organic Chemistry Laboratory, RIKEN, Saitama, Japan, 5 RIKEN Center for Sustainable Resource Science, Saitama, Japan Edited by: Xiaowu Wang, Chinese Academy of Agricultural The genus Physalis in the Solanaceae family contains several species of benefit to Sciences, China humans. Examples include P. alkekengi (Chinese-lantern plant, hôzuki in Japanese) Reviewed by: Erli Pang, used for medicinal and for decorative purposes, and P. peruviana, also known as Beijing Normal University, China Cape gooseberry, which bears an edible, vitamin-rich fruit. Members of the Physalis Zhonghua Zhang, genus are a valuable resource for phytochemicals needed for the development of Chinese Academy of Agricultural Sciences, China medicines and functional foods. To fully utilize the potential of these phytochemicals we *Correspondence: need to understand their biosynthesis, and for this we need genomic data, especially Atsushi Fukushima comprehensive transcriptome datasets for gene discovery. We report the de novo [email protected] Kazuki Saito assembly of the transcriptome from leaves of P. alkekengi and P. peruviana using [email protected] Illumina RNA-seq technologies.
  • (12) United States Patent (10) Patent No.: US 8,962,800 B2 Mathur Et Al

    (12) United States Patent (10) Patent No.: US 8,962,800 B2 Mathur Et Al

    USOO89628OOB2 (12) United States Patent (10) Patent No.: US 8,962,800 B2 Mathur et al. (45) Date of Patent: Feb. 24, 2015 (54) NUCLEICACIDS AND PROTEINS AND USPC .......................................................... 530/350 METHODS FOR MAKING AND USING THEMI (58) Field of Classification Search None (75) Inventors: Eric J. Mathur, San Diego, CA (US); See application file for complete search history. Cathy Chang, San Diego, CA (US) (56) References Cited (73) Assignee: BP Corporation North America Inc., Naperville, IL (US) PUBLICATIONS (*) Notice: Subject to any disclaimer, the term of this Nolling etal (J. Bacteriol. 183: 4823 (2001).* patent is extended or adjusted under 35 Spencer et al., “Whole-Genome Sequence Variation among Multiple U.S.C. 154(b) by 0 days. Isolates of Pseudomonas aeruginosa J. Bacteriol. (2003) 185: 1316-1325. (21) Appl. No.: 13/400,365 2002.Database Sequence GenBank Accession No. BZ569932 Dec. 17. 1-1. Mount, Bioinformatics, Cold Spring Harbor Press, Cold Spring Har (22) Filed: Feb. 20, 2012 bor New York, 2001, pp. 382-393. O O Omiecinski et al., “Epoxide Hydrolase-Polymorphism and role in (65) Prior Publication Data toxicology” Toxicol. Lett. (2000) 1.12: 365-370. US 2012/O266329 A1 Oct. 18, 2012 * cited by examiner Related U.S. Application Data - - - Primary Examiner — James Martinell (62) Division of application No. 1 1/817,403, filed as (74) Attorney, Agent, or Firm — DLA Piper LLP (US) application No. PCT/US2006/007642 on Mar. 3, 2006, now Pat. No. 8,119,385. (57) ABSTRACT (60) Provisional application No. 60/658,984, filed on Mar. The invention provides polypeptides, including enzymes, 4, 2005.

  • Generate Metabolic Map Poster

    Authors: Zheng Zhao, Delft University of Technology Marcel A. van den Broek, Delft University of Technology S. Aljoscha Wahl, Delft University of Technology Wilbert H. Heijne, DSM Biotechnology Center Roel A. Bovenberg, DSM Biotechnology Center Joseph J. Heijnen, Delft University of Technology An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Marco A. van den Berg, DSM Biotechnology Center Peter J.T. Verheijen, Delft University of Technology Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. PchrCyc: Penicillium rubens Wisconsin 54-1255 Cellular Overview Connections between pathways are omitted for legibility. Liang Wu, DSM Biotechnology Center Walter M. van Gulik, Delft University of Technology L-quinate phosphate a sugar a sugar a sugar a sugar multidrug multidrug a dicarboxylate phosphate a proteinogenic 2+ 2+ + met met nicotinate Mg Mg a cation a cation K + L-fucose L-fucose L-quinate L-quinate L-quinate ammonium UDP ammonium ammonium H O pro met amino acid a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar K oxaloacetate L-carnitine L-carnitine L-carnitine 2 phosphate quinic acid brain-specific hypothetical hypothetical hypothetical hypothetical
  • Proquest Dissertations

    Proquest Dissertations

    RICE UNIVERSITY Investigation of Triterpene Biosynthesis in Arabidopsis thaliana by Mariya D. Kolesnikova A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE Doctor of Philosophy APPROVED, THESIS COMMITTEE: Seircni P. T. Matsuda, Professor, Department Chair Department of Chemistry Department of Biochemistry and Cell Biology JU- Ronald J. Parry, Professor Department of Chemistry Department of Biochemistry and Cell Biology UL Jonatnan Silberg, ^gs&tant Profasabr Department of Biochemistry and Cell Biology HOUSTON, TEXAS May 2008 UMI Number: 3362344 INFORMATION TO USERS The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleed-through, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. UMI® UMI Microform 3362344 Copyright 2009 by ProQuest LLC All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 ii ABSTRACT Investigation of Triterpene Biosynthesis in Arabidopsis thaliana By Mariya D. Kolesnikova This thesis describes functional characterization of three oxidosqualene cyclase genes (Atlg78955, At3g45130, and At4gl5340) from the model plant Arabidopsis thaliana that encode enzymes with novel catalytic functions. Oxidosqualene cyclases are a family of membrane proteins that convert the acyclic substrate oxidosqualene into polycyclic products with many chiral centers. The complex mechanistic pathways and relevant catalytic motifs can be elucidated through judicious applications of mutagenesis, heterologous expression in combination with a genome mining approach, and protein modeling.
  • The Use of Mutants and Inhibitors to Study Sterol Biosynthesis in Plants

    The Use of Mutants and Inhibitors to Study Sterol Biosynthesis in Plants

    bioRxiv preprint doi: https://doi.org/10.1101/784272; this version posted September 26, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Title page 2 Title: The use of mutants and inhibitors to study sterol 3 biosynthesis in plants 4 5 Authors: Kjell De Vriese1,2, Jacob Pollier1,2,3, Alain Goossens1,2, Tom Beeckman1,2, Steffen 6 Vanneste1,2,4,* 7 Affiliations: 8 1: Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, 9 Belgium 10 2: VIB Center for Plant Systems Biology, VIB, Technologiepark 71, 9052 Ghent, Belgium 11 3: VIB Metabolomics Core, Technologiepark 71, 9052 Ghent, Belgium 12 4: Lab of Plant Growth Analysis, Ghent University Global Campus, Songdomunhwa-Ro, 119, Yeonsu-gu, Incheon 13 21985, Republic of Korea 14 15 e-mails: 16 K.D.V: [email protected] 17 J.P: [email protected] 18 A.G. [email protected] 19 T.B. [email protected] 20 S.V. [email protected] 21 22 *Corresponding author 23 Tel: +32 9 33 13844 24 Date of submission: sept 26th 2019 25 Number of Figures:3 in colour 26 Word count: 6126 27 28 1 bioRxiv preprint doi: https://doi.org/10.1101/784272; this version posted September 26, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
  • Dual Biosynthetic Pathways to Phytosterol Via Cycloartenol and Lanosterol in Arabidopsis

    Dual Biosynthetic Pathways to Phytosterol Via Cycloartenol and Lanosterol in Arabidopsis

    Dual biosynthetic pathways to phytosterol via cycloartenol and lanosterol in Arabidopsis Kiyoshi Ohyamaa, Masashi Suzukia, Jun Kikuchia,b,c, Kazuki Saitoa,d, and Toshiya Muranakaa,e,1 aRIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan; bGraduate School of Bioagriculture Sciences, Nagoya University, 1-1 Fro-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan; cInternational Graduate School of Integrated Sciences, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan; dGraduate School of Pharmaceutical Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan; and eKihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan Edited by Charles J. Arntzen, Arizona State University, Tempe, AZ, and approved November 21, 2008 (received for review August 5, 2008) The differences between the biosynthesis of sterols in higher HO acetyl-CoA -OOC plants and yeast/mammals are believed to originate at the cycliza- OH tion step of oxidosqualene, which is cyclized to cycloartenol in mevalonate higher plants and lanosterol in yeast/mammals. Recently, lanos- terol synthase genes were identified from dicotyledonous plant species including Arabidopsis, suggesting that higher plants pos- CAS sess dual biosynthetic pathways to phytosterols via lanosterol, and HO O through cycloartenol. To identify the biosynthetic pathway to parkeol phytosterol via lanosterol, and to reveal the contributions to 2,3-oxido- CAS squalene LAS phytosterol biosynthesis via each cycloartenol and lanosterol, we 13 2 performed feeding experiments by using [6- C H3]mevalonate with Arabidopsis seedlings. Applying 13C-{1H}{2H} nuclear magnetic resonance (NMR) techniques, the elucidation of deuterium on C-19 behavior of phytosterol provided evidence that small amounts of HO ? HO HO cycloartenol lanosterol lanosterol phytosterol were biosynthesized via lanosterol.
  • The Roles of OVATE and Other Elongation Genes in Regulating Proximal-Distal Patterning of Tomato Fruit

    The Roles of OVATE and Other Elongation Genes in Regulating Proximal-Distal Patterning of Tomato Fruit

    The roles of OVATE and other elongation genes in regulating proximal-distal patterning of tomato fruit Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Shan Wu, M.S. Graduate Program in Horticulture and Crop Science The Ohio State University 2015 Dissertation Committee: Dr. Esther van der Knaap, Advisor Dr. Jyan-chyun Jang Dr. Michelle Jones Dr. Tea Meulia Dr. Eric Stockinger Copyright by Shan Wu 2015 Abstract Domestication of tomato (Solanum lycopersicum) has resulted in a variety of fruit shapes from flat to very elongated. The elongated shape is a common feature that distinguishes many cultivated tomatoes from the undomesticated types, and it is mainly controlled by three loci, ovate, sun and fs8.1. We performed detailed morphological analyses of the reproductive and vegetative organs, which demonstrated that ovate, sun and fs8.1 regulate unique aspects of ovary and fruit elongation and in different temporal manners. The synergistic interaction between sun and ovate or fs8.1 suggested that the pathways involving SUN, OVATE and the gene(s) underlying fs8.1 may converge at a common node. We also conducted a transcriptome comparison analysis between the triple mutant sun/ovate/fs8.1 and wild type by RNA-seq using reproductive meristems and young flower buds. This study revealed changes in the transcription profile possibly caused by the combined effects of the three mutations. To gain insights into the role of OVATE in regulating fruit shape, we searched for its genetic and protein interactors. A synergistic interaction was found between ovate and suppressor of ovate 1 (sov1) in controlling ovary and fruit elongation.